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Identification Of Functional Regulatory Elements In The Human Genome Using Pooled Crispr Screens., Samantha M. Borys, Scott T. Younger

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise < 2% of the sequence space in the human genome leaving a substantial portion of the genome uninterrogated. Noncoding regions of the genome harbor important regulatory elements (e.g. promoters, enhancers, silencers) that influence cellular processes but high-throughput methods for evaluating their essentiality have yet to be established.

RESULTS: Here, we describe a CRISPR-based screening approach that facilitates the functional profiling of thousands of noncoding regulatory elements in parallel. We selected the tumor suppressor p53 as a model system and designed a pooled CRISPR library targeting thousands of p53 binding sites throughout the genome. Following transduction into dCas9-KRAB-expressing cells we identified several regulatory elements that influence cell proliferation. Moreover, …

Potential Use Of Biotherapeutic Bacteria To Target Colorectal Cancer-Associated Taxa, Gareth Lawrence, Maire Begley, Paul D. Cotter, Caitríona M. Guinane

Department of Biological Sciences Publications

The role of the gut microbiome in human health and disease is the focus of much attention. It has been widely agreed upon that our gut bacteria play a role in host immunity, nutrient absorption, digestion, metabolism, and other key drivers of health. Furthermore, certain microbial signatures and specific taxa have also been associated with the development of diseases, such as obesity; inflammatory bowel disease; and, indeed, colorectal cancer (CRC), which is the focus of this review. By extension, such taxa represent potential therapeutic targets. In particular, the emerging human pathogen Fusobacterium nucleatum represents an important agent in CRC development …

Positive Surface Charge Of Glun1 N-Terminus Mediates The Direct Interaction With Ephb2 And Nmdar Mobility., Halley R. Washburn, Nan L. Xia, Wei Zhou, Yu-Ting Mao, Matthew B. Dalva

Department of Neuroscience Faculty Papers

Localization of the N-methyl-D-aspartate type glutamate receptor (NMDAR) to dendritic spines is essential for excitatory synaptic transmission and plasticity. Rather than remaining trapped at synaptic sites, NMDA receptors undergo constant cycling into and out of the postsynaptic density. Receptor movement is constrained by protein-protein interactions with both the intracellular and extracellular domains of the NMDAR. The role of extracellular interactions on the mobility of the NMDAR is poorly understood. Here we demonstrate that the positive surface charge of the hinge region of the N-terminal domain in the GluN1 subunit of the NMDAR is required to maintain NMDARs at dendritic spine …

Trka Undergoes A Tetramer-To-Dimer Conversion To Open Trkh Which Enables Changes In Membrane Potential, M Ashley Hudson, Katrina S Hofstetter, Zhichun Xu, Mingqiang Rong, Zhao Wang, B V Venkataram Prasad, Steve W Lockless, Wah Chiu, Ming Zhou

Faculty, Staff and Students Publications

TrkH is a bacterial ion channel implicated in K+ uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting …

Week Of January 27, 2020, New York Medical College

InTouch

• NYMC Days of Giving Set for March 24 and 25
• Center for Disaster Medicine Hosts Training for White Plains Hospital
• SHSP Dean's Distinguished Leaders Lecture Series Features Leading Health Education Specialist
• Middle States Self-Study is Underway

The Mitochondrial Hsp90 Paralog Trap1 Forms An Oxphos-Regulated Tetramer And Is Involved In Mitochondrial Metabolic Homeostasis, Jungsoon Lee, Nastaran Mohammadi Ghahhari, Gregory Segala, Kristin Beebe, Lisa M Jenkins, Gaelyn C Lyons, Lilia Bernasconi, Francis T F Tsai, David A Agard, Len Neckers, Didier Picard

Faculty, Staff and Students Publications

BACKGROUND: The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. Most studies have found it to be an inhibitor of mitochondrial oxidative phosphorylation (OXPHOS) and an inducer of the Warburg phenotype of cancer cells. However, others have reported the opposite, and there is no consensus on the relevant TRAP1 interactors. This calls for a more comprehensive analysis of the TRAP1 interactome and of how TRAP1 and mitochondrial metabolism mutually affect each other.

RESULTS: We show that the disruption of the gene for TRAP1 in …

Non-Invasive Mri Quantification Of Cerebrospinal Fluid Dynamics In Amyotrophic Lateral Sclerosis Patients., Lucas R Sass, Mohammadreza Khani, Jacob Romm, Marianne Schmid Daners, Kyle Mccain, Tavara Freeman, Gregory T Carter, Douglas L Weeks, Brian Petersen, Jason Aldred, Dena Wingett, Bryn A Martin

Articles, Abstracts, and Reports

BACKGROUND: Developing novel therapeutic agents to treat amyotrophic lateral sclerosis (ALS) has been difficult due to multifactorial pathophysiologic processes at work. Intrathecal drug administration shows promise due to close proximity of cerebrospinal fluid (CSF) to affected tissues. Development of effective intrathecal pharmaceuticals will rely on accurate models of how drugs are dispersed in the CSF. Therefore, a method to quantify these dynamics and a characterization of differences across disease states is needed.

METHODS: Complete intrathecal 3D CSF geometry and CSF flow velocities at six axial locations in the spinal canal were collected by T2-weighted and phase-contrast MRI, respectively. Scans were …

Week Of January 21, 2020, New York Medical College

InTouch

• Class of 2020 Commencement Set for May 19
• Prominent Gastroenterologist to Address 24th Medical Student Research Forum
• STAR Alum is in Top 300 Scholars in the Regeneron Science Talent Search 2020

Review Of Alterations In Perlecan-Associated Vascular Risk Factors In Dementia, Amanda L. Trout, Ibolya Rutkai, Ifechukwude J. Biose, Gregory J. Bix

Neurology Faculty Publications

Perlecan is a heparan sulfate proteoglycan protein in the extracellular matrix that structurally and biochemically supports the cerebrovasculature by dynamically responding to changes in cerebral blood flow. These changes in perlecan expression seem to be contradictory, ranging from neuroprotective and angiogenic to thrombotic and linked to lipid retention. This review investigates perlecan's influence on risk factors such as diabetes, hypertension, and amyloid that effect Vascular contributions to Cognitive Impairment and Dementia (VCID). VCID, a comorbidity with diverse etiology in sporadic Alzheimer's disease (AD), is thought to be a major factor that drives the overall clinical burden of dementia. Accordingly, changes …

Protective Allele For Multiple Sclerosis Hla-Drb1*01:01 Provides Kinetic Discrimination Of Myelin And Exogenous Antigenic Peptides., Azad Mamedov, Nadezhda Vorobyeva, Ioanna Filimonova, Maria Zakharova, Ivan Kiselev, Vitalina Bashinskaya, Natalia Baulina, Alexey Boyko, Alexander Favorov, Olga Kulakova, Rustam Ziganshin, Ivan Smirnov, Alina Poroshina, Igor Shilovskiy, Musa Khaitov, Yuri Sykulev, Olga Favorova, Valentin Vlassov, Alexander Gabibov, Alexey Belogurov

Department of Microbiology and Immunology Faculty Papers

Risk of the development of multiple sclerosis (MS) is known to be increased in individuals bearing distinct class II human leukocyte antigen (HLA) variants, whereas some of them may have a protective effect. Here we analyzed distribution of a highly polymorphous HLA-DRB1 locus in more than one thousand relapsing-remitting MS patients and healthy individuals of Russian ethnicity. Carriage of HLA-DRB1*15 and HLA-DRB1*03 alleles was associated with MS risk, whereas carriage of HLA-DRB1*01 and HLA-DRB1*11 was found to be protective. Analysis of genotypes revealed the compensatory effect of risk and resistance alleles in trans. We have identified previously unknown MBP_{153−161 …}

Development And Characterization Of A Wee1 Kinase Degrader, Katherine A Donovan, Radosław P Nowak, Caitlin E Mills, David A Scott, Zainab M Doctor, Nicholas A Eleuteri, Mirra Chung, Peter K Sorger, Eric S Fischer, Nathanael S Gray

Faculty, Staff and Students Publications

The G1/S cell cycle checkpoint is frequently dysregulated in cancer, leaving cancer cells reliant on a functional G2/M checkpoint to prevent excessive DNA damage. Wee1 regulates the G2/M checkpoint by phosphorylating CDK1 at Tyr15 to prevent mitotic entry. Previous drug development efforts targeting Wee1 resulted in the clinical-grade inhibitor, AZD1775. However, AZD1775 is burdened by dose-limiting adverse events, and has off-target PLK1 activity. In an attempt to overcome these limitations, we developed Wee1 degraders by conjugating AZD1775 to the cereblon (CRBN)-binding ligand, pomalidomide. The resulting lead compound, ZNL-02-096, degrades Wee1 while sparing PLK1, induces G2/M accumulation at 10-fold lower doses …

Hypercholesterolemia Accelerates Both The Initiation And Progression Of Angiotensin Ii-Induced Abdominal Aortic Aneurysms, Jing Liu, Hisashi Sawada, Deborah A. Howatt, Jessica J. Moorleghen, Olga A. Vsevolozhskaya, Alan Daugherty, Hong S. Lu

Pharmacology and Nutritional Sciences Faculty Publications

Objective: This study determined whether hypercholesterolemia would contribute to both the initiation and progression of angiotensin (Ang)II-induced abdominal aortic aneurysms (AAAs) in mice.

Methods and Results: To determine whether hypercholesterolemia accelerates the initiation of AAAs, male low-density lipoprotein (LDL) receptor -/- mice were either fed one week of Western diet prior to starting AngII infusion or initiated Western diet one week after starting AngII infusion. During the first week of AngII infusion, mice fed normal diet had less luminal expansion of the suprarenal aorta compared to those initiated Western diet after the first week of AngII infusion. The two groups …

Week Of January 13, 2020, New York Medical College

InTouch

• Ira J. Bedzow, Ph.D., is Named UNESCO Chair of Bioethics
• Department of Surgery Hosts Sixteenth Annual Louis R.M. Del Guercio, M.D., Distinguished Visiting Professorship and Research Day
• Graduate Student Association Aims to Enhance Student Life
• Center for Disaster Medicine Hosts Pediatric Focused Disaster Response Training

Frontotemporal Dementia Nonsense Mutation Of Progranulin Rescued By Aminoglycosides, Lisha Kuang, Kei Hashimoto, Eric J. Huang, Matthew S. Gentry, Haining Zhu

Molecular and Cellular Biochemistry Faculty Publications

Frontotemporal dementia (FTD) is an early onset dementia and is characterized by progressive atrophy of the frontal and/or temporal lobes. FTD is highly heritable with mutations in progranulin accounting for 5-26% of cases in different populations. Progranulin is involved in endocytosis, secretion and lysosomal processes, but its function under physiological and pathological conditions remains to be defined. Many FTD-causing nonsense progranulin mutations contain a premature termination codon (PTC), thus progranulin haploinsufficiency has been proposed as a major disease mechanism. Currently, there is no effective FTD treatment or therapy.

Aminoglycosides are a class of antibiotics that possess a less known function …

Generation Of In-Frame Gene Deletion Mutants In Pseudomonas Aeruginosa And Testing For Virulence Attenuation In A Simple Mouse Model Of Infection, Meagan E. Valentine, Brandon D. Kirby, Hongwei D. Yu

Biomedical Sciences

Microorganisms are genetically versatile and diverse and have become a major source of many commercial products and biopharmaceuticals. Though some of these products are naturally produced by the organisms, other products require genetic engineering of the organism to increase the yields of production. Avirulent strains of Escherichia coli have traditionally been the preferred bacterial species for producing biopharmaceuticals; however, some products are difficult for E. coli to produce. Thus, avirulent strains of other bacterial species could provide useful alternatives for production of some commercial products. Pseudomonas eruginosa is a common and well-studied Gram-negative bacterium that could provide a suitable alternative …

Investigating The Potential And Pitfalls Of Ev-Encapsulated Micrornas As Circulating Biomarkers Of Breast Cancer, Brian M. Moloney, Katie E. Gilligan, Doireann P. Joyce, Clodagh P. O'Neill, Killian P. O'Brien, Sonja Khan, Claire L. Glynn, Ronan M. Waldron, Ciarán M. Maguire, Emma Holian, Erin Naughton, Mohamed Elhadi, Andrea B. Grealish, Carmel Malone, Emma Mcdermott, Peter Dockery, Thomas Ritter, Adriele Prina-Mello, Michael J. Kerin, Róisín M. Dwyer

Forensic Science Publications

Extracellular vesicles (EVs) shuttle microRNA (miRNA) throughout the circulation and are believed to represent a fingerprint of the releasing cell. We isolated and characterized serum EVs of breast tumour-bearing animals, breast cancer (BC) patients, and healthy controls. EVs were characterized using transmission electron microscopy (TEM), protein quantification, western blotting, and nanoparticle tracking analysis (NTA). Absolute quantitative (AQ)-PCR was employed to analyse EV-miR-451a expression. Isolated EVs had the appropriate morphology and size. Patient sera contained significantly more EVs than did healthy controls. In tumour-bearing animals, a correlation between serum EV number and tumour burden was observed. There was no significant relationship …

Allele-Specific Expression Changes Dynamically During T Cell Activation In Hla And Other Autoimmune Loci, M. Gutierrez-Arcelus, Y. Baglaenko, J. Arora, S. Hannes, Y. Luo, T. Amariuta, N. Teslovich, D. A. Rao, P. K. Gregersen, S. Raychaudhuri, +8 Additional Authors

Journal Articles

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Genetic studies have revealed that autoimmune susceptibility variants are over-represented in memory CD4+ T cell regulatory elements1–3. Understanding how genetic variation affects gene expression in different T cell physiological states is essential for deciphering genetic mechanisms of autoimmunity4,5. Here, we characterized the dynamics of genetic regulatory effects at eight time points during memory CD4+ T cell activation with high-depth RNA-seq in healthy individuals. We discovered widespread, dynamic allele-specific expression across the genome, where the balance of alleles changes over time. These genes were enriched fourfold within autoimmune loci. …

Celebrating 20 Years Of Ighv Mutation Analysis In Cll., N. Chiorazzi, F. K. Stevenson

Journal Articles

The division of CLL into 2 broad subsets with highly significant differences in clinical behavior was reported in 2 landmark papers in Blood in 1999.1,2 The simple analysis of the mutational status of the IGV regions provided both a prognostic indicator and an insight into the cellular origins. Derivation from B cells with very low or no IGV mutations generally leads to a more aggressive disease course than derivation from B cells with higher levels. This finding focused attention on surface Ig (sIg), the major B-cell receptor, and revealed dynamic antigen engagement in vivo as a tumor driver. It has …

Fusion, 2020, George Washington University, William H. Beaumont Medical Research Honor Society

Fusion

No abstract provided.

Steroid Resistance In Diamond Blackfan Anemia Associates With P57(Kip2) Dysregulation In Erythroid Progenitors, R. J. Ashley, H. Yan, N. Wang, J. Hale, B. M. Dulmovits, J. Papoin, M. E. Olive, A. Vlachos, J. M. Lipton, L. Blanc, +8 Additional Authors

Journal Articles

No abstract provided.

Ultrasound Powered Piezoelectric Neurostimulation Devices: A Commentary., T. Sun, J. Wright, T. Datta-Chaudhuri

Journal Articles

Conventional neurostimulation systems for preclinical research can be bulky and invasive due to the need for batteries or wired interfaces. Emerging as a new neural interface technique, ultrasound-powered piezoelectric neural stimulators work by converting ultrasound energy to electrical charge for neural stimulation. In addition to the benefits of wireless powering and miniaturization leading to less traumatic surgery, piezoelectric neural stimulators can also exhibit prolonged operational lifetimes for a long-term stable neural interface, and show promise for clinical translation. As one of first steps to demonstrate the value of ultrasound-powered piezoelectric neural interface, Li et al. developed a piezoelectric stimulator to …

Neutrophils Are Mediators Of Metastatic Prostate Cancer Progression In Bone, Diane L. Costanzo-Garvey, Tyler Keeley, Adam J. Case, Gabrielle F. Watson, Massar Alsamraae, Yangsheng Yu, Kaihong Su, Cortney E. Heim, Tammy Kielian, Colm Morrissey, Jeremy S Frieling, Leah M. Cook

Journal Articles: Pathology and Microbiology

Bone metastatic prostate cancer (BM-PCa) significantly reduces overall patient survival and is currently incurable. Current standard immunotherapy showed promising results for PCa patients with metastatic, but less advanced, disease (i.e., fewer than 20 bone lesions) suggesting that PCa growth in bone contributes to response to immunotherapy. We found that: (1) PCa stimulates recruitment of neutrophils, the most abundant immune cell in bone, and (2) that neutrophils heavily infiltrate regions of prostate tumor in bone of BM-PCa patients. Based on these findings, we examined the impact of direct neutrophil-prostate cancer interactions on prostate cancer growth. Bone marrow neutrophils directly induced apoptosis …

Stochastic Expression Of Sae-Dependent Virulence Genes During Staphylococcus Aureus Biofilm Development Is Dependent On Saes, Elizabeth A. Delmain, Derek E. Moormeier, Jennifer L. Endres, Rebecca E. Hodges, Marat R. Sadykov, Alexander R. Horswill, Kenneth W. Bayles

Journal Articles: Pathology and Microbiology

The intricate process of biofilm formation in the human pathogen Staphylococcus aureus involves distinct stages during which a complex mixture of matrix molecules is produced and modified throughout the developmental cycle. Early in biofilm development, a subpopulation of cells detaches from its substrate in an event termed “exodus” that is mediated by SaePQRS-dependent stochastic expression of a secreted staphylococcal nuclease, which degrades extracellular DNA within the matrix, causing the release of cells and subsequently allowing for the formation of metabolically heterogenous microcolonies. Since the SaePQRS regulatory system is involved in the transcriptional control of multiple S. aureus virulence factors, the …

First-Time Characterization Of Viable But Non-Culturable Proteus Mirabilis: Induction And Resuscitation, Reham Wasfi, G. R. Abdellatif, H. M. Elshishtawy, Hossam M. Ashour

USF St. Petersburg Campus Faculty Publications

Pathogenic bacteria can enter into a viable but non-culturable (VBNC) state under unfavourable conditions. Proteus mirabilis is responsible for dire clinical consequences including septicaemia, urinary tract infections and pneumonia, but is not a species previously known to enter VBNC state. We suggested that stress-induced P. mirabilis can enter a VBNC state in which it retains virulence. P. mirabilis isolates were incubated in extreme osmotic pressure, starvation, low temperature and low pH to induce a VBNC state. Resuscitation was induced by temperature upshift and inoculation in tryptone soy broth with Tween 20 and brain heart infusion broth. Cellular ultrastructure and gene …

Social Media Engagement At Academic Conferences: Report Of The Association Of Pathology Chairs 2018 And 2019 Annual Meeting Social Media Committee, Yonah C. Ziemba, Dana Razzano, Timothy C. Allen, Adam L. Booth, Scott R. Anderson, Anne Champeaux, Michael D. Feldman, Valerie Fitzhugh, Simone Gittens, Marilea Grider, Mary Gupta, Christina Hanos, Karen Kelly, Tarush Kothari, Jennifer Laudadio, Amy Y. Lin, Kamran M. Mirza, Kathleen T. Montone, Priscilla S. Markwood

Pathology and Cell Biology Faculty Publications

The use of social media at academic conferences is expanding, and platforms such as Twitter are used to share meeting content with the world. Pathology conferences are no exception, and recently, pathology organizations have promoted social media as a way to enhance meeting exposure. A social media committee was formed ad hoc to implement strategies to enhance social media involvement and coverage at the 2018 and 2019 annual meetings of the Association of Pathology Chairs. This organized approach resulted in an 11-fold increase in social media engagement compared to the year prior to committee formation (2017). In this article, the …

Identifying Factors Underlying The Decision For Genetic Carrier Screening Among Women In Montgomery County, Sowon Kim

Scholarship in Medicine - All Papers

As medical scientific technologies evolve, numerous medical tests help not only physicians with their clinical judgment, but also patients by empowering them with more knowledge of their own health. An example is Genetic Carrier Screening (GCS) [1-2]. Genetic Carrier Screening (GCS) is a genetic test that allows patients to find out if they carry genes for certain genetic disorders. The results of the test enable patients to make changes to their family planning decisions and prenatal care when appropriate and allow them the opportunity to seek further medical and social support [3]. The clinical utility of GCS is evident in …

Rab27 And 14-3-3 Mediated Regulation Of Alpha-Synuclein Pathology, Rachel Nicole Underwood

All ETDs from UAB

Alpha-synuclein (αsyn) is the key component of proteinaceous aggregates termed Lewy Bodies (LBs) that pathologically define a group of disorders known as synucleinopathies, including Parkinson’s Disease (PD) and Dementia with Lewy Bodies (DLB). αSyn is thought to misfold and spread throughout the brain in a prion-like fashion. Transmission of αsyn necessitates the release of misfolded αsyn from one cell and the uptake of that αsyn by another, in which it templates the misfolding of endogenous αsyn. Identifying regulators of this process is essential to understanding how αsyn propagates and furthers disease progression. In this study, we investigated Rab27 and 14-3-3θ …

Co-Factors In Fgf Signaling, Christopher Yanucil

All ETDs from UAB

The fibroblast growth factor (FGF) family consists of a group of proteins whose diverse biological functions are mediated by receptor tyrosine kinases, termed FGF receptors (FGFR) 1-4. While paracrine FGFs require heparin sulfate as a co-factor for FGFR bind-ing and signaling, it has been assumed that endocrine FGFs, such as FGF23, do not bind heparin but instead require klotho, a family of transmembrane proteins, as a co-receptor on specific target cells. FGF23 acts as bone-derived hormone that targets tubular epitheli-al cells in the kidney via FGFR1 and α-klotho to reduce renal phosphate uptake. In chron-ic kidney disease (CKD), the kidney …

Advancing Single Cell And Crispr/Dcas9 Technologies For The Study Of Reward Learning And Addiction, Corey Grant Duke

All ETDs from UAB

Drug addiction is a chronic relapsing condition inflicting tremendous harm to individuals and society with ineffective treatment options available to most people. Drugs of abuse elevate dopamine levels in a brain region known as the nucleus accumbens (NAc), and activate gene programs considered essential for producing lasting synaptic and cell state changes which underlie the generation of addictive behavior. These gene expression changes remain poorly understood due to a complex heterogenous cellular architecture, and the rapidly fluctuating nature of the transcriptional processes themselves which make investigation difficult. Recent technical advances increase access to both profiling and manipulating these transcriptional changes …

Utilizing Social Media To Spread Knowledge: The Association Of Pathology Chairs Experience At The 2018 Annual Meeting, Dana Razzano, Yonah C. Ziemba, Adam L. Booth, Priscilla Markwood, Christina T. Hanos, Nicole Riddle

Pathology and Cell Biology Faculty Publications

No abstract provided.